I see that your config contains "TT" RAM for the Falcon. Can you test if
the issue vanishes if you remove the TT RAM from the configuration? If
so, this might point to the reason. On a real Falcon, the floppy DMA
doesn't support RAM above the 16 MiB mark.
Ooh, this was nice. Hats off for another great analysis. Even if I'm aware of this, I would have never connected the dots, wow. So all those years... it was this reason. :-)
Not sure how easy / desired it is to fix on Hatari's side, strictly speaking its not a Hatari bug but IIRC every hardware accelerator which provided some TT RAM had it fixed somehow (I think it has to provide _FRB but this must be used by the device driver which is in this case the GEMDOS HD emulator?)
Does the issue occur when you use EmuTOS on the emulated Falcon?
That's the thing, EmuTOS is usually so feature-packed that I don't need any driver / bootstrap disk when using it. :-)